Hi Ankit,

I am not aware of any methods for methylation arrays that can infer DNA methylation at sites with C>T SNPs or mutations.

If you have bisulfite sequencing data from a directional protocol, you can measure DNA methylation at C>T SNPs/mutated sites. As neatly explained in the Bis-SNP paper (Liu et al., 2020. Genome Biology, see Figure 1):

A key property of some bisulfite-related protocols is that G nucleotides on the strand opposing a C are not affected by conversion. This strand-specificity principle has been exploited in order to distinguish bisulfite conversion from C>T SNPs.... approximately half the reads at a given cytosine position [mapping to C] can be used for methylation quantification.... the other half [mapping to G] can be used to identify C>T SNPs.

We recently released a tool for RRBS (and now WGBS) that takes these SNPs and mutations into account when processing methylation data (Larose Cadiuex et al., 2022. bioRxiv).

Hope that helps!